rs692607

Variant names:

• chr11-50420232-T-C
• rs692607
• ENST00000532521.2:n.579T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-50420232-T-C
• chr11-50420232-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532521.2(ENSG00000214883):​n.579T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 1,076,986 control chromosomes in the GnomAD database, including 176,765 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (22061 hom., cov: 32)
  • Exomes 𝑓: 0.57 (154704 hom.)
• Consequence: ENSG00000214883 ENST00000532521.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.03
• Publications: 7 publications found

Genes affected

ENSG00000214883 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC646813	NR_024504.2	n.435T>C		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000214883	ENST00000532521.2	n.579T>C		non_coding_transcript_exon_variant	Exon 5 of 8	6

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79654 AN: 151310 Hom.: 22055 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.583

GnomAD4 exome AF: 0.575 AC: 531757 AN: 925558 Hom.: 154704 Cov.: 11 AF XY: 0.576 AC XY: 273150 AN XY: 474572

African (AFR) AF: 0.377 AC: 7138 AN: 18952

American (AMR) AF: 0.676 AC: 16848 AN: 24926

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 11686 AN: 17234

East Asian (EAS) AF: 0.543 AC: 18044 AN: 33216

South Asian (SAS) AF: 0.560 AC: 29836 AN: 53296

European-Finnish (FIN) AF: 0.581 AC: 26483 AN: 45566

Middle Eastern (MID) AF: 0.664 AC: 2933 AN: 4414

European-Non Finnish (NFE) AF: 0.575 AC: 395422 AN: 687350

Other (OTH) AF: 0.575 AC: 23367 AN: 40604

GnomAD4 genome AF: 0.526 AC: 79685 AN: 151428 Hom.: 22061 Cov.: 32 AF XY: 0.528 AC XY: 39036 AN XY: 73966

African (AFR) AF: 0.379 AC: 15581 AN: 41128

American (AMR) AF: 0.640 AC: 9734 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2302 AN: 3460

East Asian (EAS) AF: 0.533 AC: 2721 AN: 5104

South Asian (SAS) AF: 0.534 AC: 2567 AN: 4808

European-Finnish (FIN) AF: 0.572 AC: 6028 AN: 10542

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38729 AN: 67864

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

Alfa AF: 0.538 Hom.: 3432

Bravo AF: 0.527

Asia WGS AF: 0.501 AC: 1744 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.30
PhyloP100		3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs692607; hg19: chr11-50379403;